Li, M.H.
(Animal Production Research, MTT Agrifood Research Finland)
,
Nogovitsina, E.
(Yakut State Agricultural Academy)
,
Ivanova, Z.
(Yakut State Agricultural Academy)
,
Erhardt, G.
(Institute for Animal Breeding and Genetics, Justus-Liebig University)
,
Vilkki, J.
(Animal Production Research, MTT Agrifood Research Finland)
,
Popov, R.
(Department of Farm Animals and Breeding, Ministry of Agriculture and Resources of Sakha)
,
Ammosov, I.
(Batagay-Alyta)
,
Kiselyova, T.
(All-Russian Research Institute for Farm Animal Genetics and Breeding, Department of Biotechnology)
,
Kantanen, J.
(Animal Production Research, MTT Agrifood Research Finland)
Indigenous Yakutian cattle' adaptation to the hardest subarctic conditions makes them a valuable genetic resource for cattle breeding in the Siberian area. Since early last century, crossbreeding between native Yakutian cattle and imported Simmental and Kholmogory breeds has been widely adopted. In ...
Indigenous Yakutian cattle' adaptation to the hardest subarctic conditions makes them a valuable genetic resource for cattle breeding in the Siberian area. Since early last century, crossbreeding between native Yakutian cattle and imported Simmental and Kholmogory breeds has been widely adopted. In this study, variations at 22 polymorphic microsatellite loci in 5 populations of Yakutian, Kholmogory, Simmental, Yakutian-Kholmogory and Yakutian-Simmental cattle were analysed to estimate the genetic contribution of Yakutian cattle to the two hybrid populations. Three statistical approaches were used: the weighted least-squares (WLS) method which considers all allele frequencies; a recently developed implementation of a Markov chain Monte Carlo (MCMC) method called likelihood-based estimation of admixture (LEA); and a model-based Bayesian admixture analysis method (STRUCTURE). At population-level admixture analyses, the estimate based on the LEA was consistent with that obtained by the WLS method. Both methods showed that the genetic contribution of the indigenous Yakutian cattle in Yakutian-Kholmogory was small (9.6% by the LEA and 14.2% by the WLS method). In the Yakutian-Simmental population, the genetic contribution of the indigenous Yakutian cattle was considerably higher (62.8% by the LEA and 56.9% by the WLS method). Individual-level admixture analyses using STRUCTURE proved to be more informative than the multidimensional scaling analysis (MDSA) based on individual-based genetic distances. Of the 9 Yakutian-Simmental animals studied, 8 showed admixed origin, whereas of the 14 studied Yakutian-Kholmogory animals only 2 showed Yakutian ancestry (>5%). The mean posterior distributions of individual admixture coefficient (q) varied greatly among the samples in both hybrid populations. This study revealed a minor existing contribution of the Yakutian cattle in the Yakutian-Kholmogory hybrid population, but in the Yakutian-Simmental hybrid population, a major genetic contribution of the Yakutian cattle was seen. The results reflect the different crossbreeding patterns used in the development of the two hybrid populations. Additionally, molecular evidence for differences among individual admixture proportions was seen in both hybrid populations, resulting from the stochastic process in crossing over generations.
Indigenous Yakutian cattle' adaptation to the hardest subarctic conditions makes them a valuable genetic resource for cattle breeding in the Siberian area. Since early last century, crossbreeding between native Yakutian cattle and imported Simmental and Kholmogory breeds has been widely adopted. In this study, variations at 22 polymorphic microsatellite loci in 5 populations of Yakutian, Kholmogory, Simmental, Yakutian-Kholmogory and Yakutian-Simmental cattle were analysed to estimate the genetic contribution of Yakutian cattle to the two hybrid populations. Three statistical approaches were used: the weighted least-squares (WLS) method which considers all allele frequencies; a recently developed implementation of a Markov chain Monte Carlo (MCMC) method called likelihood-based estimation of admixture (LEA); and a model-based Bayesian admixture analysis method (STRUCTURE). At population-level admixture analyses, the estimate based on the LEA was consistent with that obtained by the WLS method. Both methods showed that the genetic contribution of the indigenous Yakutian cattle in Yakutian-Kholmogory was small (9.6% by the LEA and 14.2% by the WLS method). In the Yakutian-Simmental population, the genetic contribution of the indigenous Yakutian cattle was considerably higher (62.8% by the LEA and 56.9% by the WLS method). Individual-level admixture analyses using STRUCTURE proved to be more informative than the multidimensional scaling analysis (MDSA) based on individual-based genetic distances. Of the 9 Yakutian-Simmental animals studied, 8 showed admixed origin, whereas of the 14 studied Yakutian-Kholmogory animals only 2 showed Yakutian ancestry (>5%). The mean posterior distributions of individual admixture coefficient (q) varied greatly among the samples in both hybrid populations. This study revealed a minor existing contribution of the Yakutian cattle in the Yakutian-Kholmogory hybrid population, but in the Yakutian-Simmental hybrid population, a major genetic contribution of the Yakutian cattle was seen. The results reflect the different crossbreeding patterns used in the development of the two hybrid populations. Additionally, molecular evidence for differences among individual admixture proportions was seen in both hybrid populations, resulting from the stochastic process in crossing over generations.
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문제 정의
This study demonstrates the utility of these approaches for estimating admixture proportions in crossbred domestic animal populations. The results of the population-level admixture analysis showed that the Yakutian-Kholmogory cattle population contained a low proportion of genetic contribution from the indigenous Yakutian cattle, while a strong contribution of the Yakutian cattle was detected in the Yakutian-Simmental hybrid population.
This study demonstrates the utility of these approaches for estimating admixture proportions in crossbred domestic animal populations.
제안 방법
In this study, the main purpose was to estimate the admixture proportions of the indigenous Yakutian cattle in two contemporary hybrid cattle populations in the Sakha Republic by using population and individual level admixture analyses. Multidimensional scaling analysis (MDSA) based on Nei’s (1978) standard genetic distances among all samples was performed for assessing the genetic structure in the cattle populations independent of any prior classification.
To combine their adaptability with productivity, they have been crossed with the Simmental and Kholmogory cattle breeds on a large scale from the year 1929 onwards (Dmitriev and Ernst, 1989). In this study, two hybrid populations of the Yakutian-Simmental and Yakutian-Kholmogory cattle breeds, established by continuous crossbreeding between native Yakutian cattle and East Siberian populations of Simmental and Kholmogory cattle, were analysed for their genetic admixture. In the Megino-Kangalasskyi region (61°N 130°E), the Yakutian-Simmental hybrid population had been formed by crossing commercial Simmental cows with local Yakutian bulls followed by inter se breeding of the first crossbred generations since 1995.
For this analysis we used the last two options. The posterior distribution of individual admixture coefficient (q) and their 90% probability intervals were estimated by assuming an admixture model with two parental populations, namely, the indigenous Yakutian cattle population and the Kholmogory or the Simmental cattle population. The mean posterior distribution of the individual admixture coefficient had been denoted q and represented an estimate of the amount of an individual's genome that was derived from one of the parental populations.
The posterior distribution of individual admixture coefficient (q) and their 90% probability intervals were estimated by assuming an admixture model with two parental populations, namely, the indigenous Yakutian cattle population and the Kholmogory or the Simmental cattle population.
대상 데이터
In each run, we used the STRUCTURE with K=2 (K is the number of the populations assumed to have contributed to the gene pool of the hybrid population) to compute the ancestry. A burn-in period of 50,000 steps, which was followed by 100,000 MCMC replicates, was used here. A threshold value of 有 >0.
In each run, we used the STRUCTURE with K=2 (K is the number of the populations assumed to have contributed to the gene pool of the hybrid population) to compute the ancestry. A burn-in period of 50,000 steps, which was followed by 100,000 MCMC replicates, was used here. A threshold value of 有 >0.
A total of 22 microsatellite loci were included in this investigation: BoLA-DRBPl, HEL10, BM1818, BM1824, BM2113, ETH3, ETH10, ETH152, ETH225, HEL1, HEL5, HEL9, HEL13, ILSTS005, ILSTS006, INRA005, INRA023, INRA032, INRA035, INRA037, INRA063 and CSSM66. The latter 20 loci have been selected from a list of 30 recommended for collaborative genetic diversity studies (http://www.
Data for 22 microsatellite DNA loci were collected from 169 cattle individuals representing 5 populations. Two hybrid cattle populations, the Yakutian-Simmental (YS; n=9) and the Yakutian-Kholmogory (YK; n=14), were collected on the collective farm “Krasnaya Zvezda” in the MeginoKangalasskyi region and on the farm “Edei” of the “Edeisky” collective agricultural enterprise in the Namsky region of the Sakha Republic, northeast of Russia, respectively.
이론/모형
, 2004). Each analysis was based on 100,000 MCMC steps and the results were reported as likelihood curves estimated by using the program Locifit (Loader, 1996) as implemented in the Locifit package for R v. 1.0. We chose the point having the highest density as an estimate of the genetic contribution by the indigenous Yakutian cattle, in parallel with 90% probability intervals of the posterior distribution of admixture proportions.
Genetic relationships among individuals of the whole sample set (n=169) were described by a multidimensional scaling analysis (MDSA), which was carried out based on a matrix of Nei’s (1978) standard genetic distances among all individuals, using the program VISTA 5.6.3 (Young, 1996). In this analysis, population clusters are identified graphically and it is not possible to assign the individuals to the clusters quantitatively (probabilistically) (Pierpaoli et al.
In individual-level admixture analyses the individual admixture coefficient (q) was assessed by using a modelbased Bayesian procedure, implemented in the program STRUCTURE (Pritchard et al., 2000). The program STRUCTURE is a Markov chain Monte Carlo approach that clusters individuals to minimize Hardy-Weinberg disequilibrium and gametic phase disequilibrium between loci within groups (Pritchard et al.
성능/효과
However, a look at the standard errors obtained with the two population-level analysis methods showed conflicting results: 2.2% by the LEA and 8.9% by the WSL method in the Yakutian-Kholmogory hybrid population, 5.4% by the LEA and 1.7% by the WSL method in the YakutianSimmental hybrid population. Neither of the two methods seemed to indicate a much greater certainty on the value of q than the other one.
However, a look at the standard errors obtained with the two population-level analysis methods showed conflicting results: 2.2% by the LEA and 8.9% by the WSL method in the Yakutian-Kholmogory hybrid population, 5.4% by the LEA and 1.7% by the WSL method in the YakutianSimmental hybrid population. Neither of the two methods seemed to indicate a much greater certainty on the value of q than the other one.
4% Yakutian cattle ancestry were completely identical to the pure Kholmogory cattle. In conclusion, the analysis showed the presence of two individuals with admixed origin and a very small genetic contribution of the indigenous Yakutian cattle in most animals of the contemporary Yakutian-Kholmogory cattle population.
In the case of population-level admixture analysis, we are interested in the fraction of genes in the admixed population that comes from one or other of the parental population. The results of both the WLS and LEA methods showed that the contribution of the indigenous Yakutian cattle in the Yakutian-Kholmogory hybrid population (9.6% by the LEA and 14.2% by the WLS method) was smaller than that in the Yakutian-Simmental hybrid population (62.8% by LEA and 56.9% by WLS). This is concordant with the known history of backcrossing with Kholmogory bulls as the recurrent parent in the Yakutian-Kholmogory hybrid population.
This study demonstrates the utility of these approaches for estimating admixture proportions in crossbred domestic animal populations. The results of the population-level admixture analysis showed that the Yakutian-Kholmogory cattle population contained a low proportion of genetic contribution from the indigenous Yakutian cattle, while a strong contribution of the Yakutian cattle was detected in the Yakutian-Simmental hybrid population. Further, as illustrated by the individual-level admixture analysis, the contributions of the Yakutian cattle in animals of both hybrid populations differed greatly.
, 2001). The results showed a small genetic contribution of the indigenous Yakutian cattle in the Yakutian-Kholmogory cattle population, pointing to a value of P1=9.6% (90% probability interval: 1.0%-19.4%) (Figure 3a). However, a look at the genetic contribution of the indigenous Yakutian cattle in the Yakutian-Simmental hybrid population showed a much higher admixture proportion of P1=62.
The slopes of the regression lines (0.142 and 0.569), which were in good agreement with the data points, gave estimates of the proportions of genes from the indigenous Yakutian cattle in the Yakutian-Kholmogory (14.2%) and the Yakutian-Simmental (56.9%) hybrid populations, respectively.
The difference in allele frequencies between the indigenous Yakutian cattle population and each hybrid population, plotted against the difference in allele frequencies between the parental populations for all the alleles encountered at the 22 loci surveyed, are shown in Figure 2. The slopes of the regression lines (0.142 and 0.569), which were in good agreement with the data points, gave estimates of the proportions of genes from the indigenous Yakutian cattle in the Yakutian-Kholmogory (14.2%) and the Yakutian-Simmental (56.9%) hybrid populations, respectively. The goodness of fit of the linear admixture model for the present data was also revealed by the graphical displays (Figure 2).
5%) (Figure 3b). The standard errors of the estimates obtained with this method were 5.4% (Yakutian-Kholmogory) and 1.7% (YakutianSimmental).
5%) (Figure 3b). The standard errors of the estimates obtained with this method were 5.4% (Yakutian-Kholmogory) and 1.7% (YakutianSimmental).
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